A series of molecular dynamics and homology modeling computer labs for an undergraduate molecular modeling course

Biochemistry and Molecular Biology Education : a Bimonthly Publication of the International Union of Biochemistry and Molecular Biology
Donald E ElmoreMadeleine E Kieffer

Abstract

As computational modeling plays an increasingly central role in biochemical research, it is important to provide students with exposure to common modeling methods in their undergraduate curriculum. This article describes a series of computer labs designed to introduce undergraduate students to energy minimization, molecular dynamics simulations, and homology modeling. These labs were created as part of a one-semester course on the molecular modeling of biochemical systems. Students who completed these activities felt that they were an effective component of the course, reporting improved comfort with the conceptual background and practical implementation of the computational methods. Although created as a component of a larger course, these activities could be readily adapted for a variety of other educational contexts. As well, all of these labs utilize software that is freely available in an academic environment and can be run on fairly common computer hardware, making them accessible to teaching environments without extensive computational resources.

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Citations

Nov 11, 2011·PloS One·Nannette Y YountMichael R Yeaman
Jan 24, 2016·Biochemistry and Molecular Biology Education : a Bimonthly Publication of the International Union of Biochemistry and Molecular Biology·Sanchita Hati, Sudeep Bhattacharyya
Dec 8, 2015·Biochemistry and Molecular Biology Education : a Bimonthly Publication of the International Union of Biochemistry and Molecular Biology·Urmi Roy
Mar 24, 2016·Biochemistry and Molecular Biology Education : a Bimonthly Publication of the International Union of Biochemistry and Molecular Biology·Donald E Elmore
Nov 22, 2013·Biochemistry and Molecular Biology Education : a Bimonthly Publication of the International Union of Biochemistry and Molecular Biology·Harry ChiangTroy C Messina
Oct 30, 2013·Biochemistry and Molecular Biology Education : a Bimonthly Publication of the International Union of Biochemistry and Molecular Biology·Fernanda BadottiMainá Bitar
Sep 9, 2020·Biochemistry and Molecular Biology Education : a Bimonthly Publication of the International Union of Biochemistry and Molecular Biology·Febdian RusydiAndrivo Rusydi
Nov 22, 2018·Biochemistry and Molecular Biology Education : a Bimonthly Publication of the International Union of Biochemistry and Molecular Biology·Julie B Ealy
Dec 24, 2018·Biochemistry and Molecular Biology Education : a Bimonthly Publication of the International Union of Biochemistry and Molecular Biology·Paula Alvarez AbreuHelena Carla Castro
Apr 13, 2021·Biochemistry and Molecular Biology Education : a Bimonthly Publication of the International Union of Biochemistry and Molecular Biology·Gonçalo C JustinoMarta C Justino

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